Origin IGS: taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 cagcattgttcgtttatcgcgaacaatgtgcttggtttccttgacgacaaatgaaataaactgcttcatctatattgaacatttatattgaggtgtattctta Mask Tandem Repeat Region ================================================ taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Find is-nt database================================================ Query_seq: PI0531:PI0532|PI0531:PI0532:ABC transporter, ATP-binding protein; possible gliding motility related:ABC transporter, ATP-binding/permease protein:->->:486300..486402 103 taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: PI0531:PI0532|PI0531:PI0532:ABC transporter, ATP-binding protein; possible gliding motility related:ABC transporter, ATP-binding/permease protein:->->:486300..486402 103 taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: PI0531:PI0532|PI0531:PI0532:ABC transporter, ATP-binding protein; possible gliding motility related:ABC transporter, ATP-binding/permease protein:->->:486300..486402 103 taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Predict ORF larger than 30AA ================================================ taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: PI0531:PI0532|PI0531:PI0532:ABC transporter, ATP-binding protein; possible gliding motility related:ABC transporter, ATP-binding/permease protein:->->:486300..486402 103 taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Intra-Species Hit: Count: 1 Min: 1 Max: 103 Len: 103 Subject: pint_PI0531_PI0532|ABC transporter, ATP-binding protein; possible gliding motility related:ABC transporter, ATP-binding/permease protein|POSITIVE:POSITIVE|[486300,486402]|103 HSP 1 e-value: 4.0E-52 bit: 204.0 Len: 103 Query Start:1 Query End:103 Subject Strand: POSITIVE Subject Start: 1 Subject End: 103 taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg taagaatacacctcaatataaatgttcaatatagatgaagcagtttatttcatttgtcgtcaaggaaaccaagcacattgttcgcgataaacgaacaatgctg Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAAGAAUACACCUCAAUAUAAAUGUUCAAUAUAGAUGAAGCAGUUUAUUUCAUUUGUCGUCAAGGAAACCAAGCACAUUGUUCGCGAUAAACGAACAAUGCUG ..........(((..(((((((((......((((((......))))))..))))))).))..)))......((((..(((((((.......))))))))))). (-19.00) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ CAGCAUUGUUCGUUUAUCGCGAACAAUGUGCUUGGUUUCCUUGACGACAAAUGAAAUAAACUGCUUCAUCUAUAUUGAACAUUUAUAUUGAGGUGUAUUCUUA ..(((((((((((.....))))))))))).....(((((.(((....)))..))))).....((((((..((((.........)))).))))))......... (-21.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 283 89 48 88 41 pint:PI1496|5end_nucleoside_phosphorylase_1417116..1417346_POSITIVE 274 93 52 100 51 pint:PI1911|5end_ribosomal_protein_S20_1855904..1856134_POSITIVE 263 80 33 135 82 pint:PI0041|5end_hypothetical_protein_41785..42015_POSITIVE 262 76 36 69 24 pint:PI1329|5end_dTDP-glucose_4,6-dehydratase_1246729..1246959_POSITIVE 262 100 53 167 116 pint:PI0683|5end_hypothetical_protein_619292..619522_POSITIVE 261 90 56 180 151 pint:PI0676|5end_hypothetical_protein_614576..614806_POSITIVE 260 85 51 206 168 pint:PI1448|5end_hypothetical_protein_1371579..1371809_POSITIVE 254 96 52 71 28 pint:PI0197|5end_acetate_kinase_188602..188832_POSITIVE 240 76 34 64 23 pint:PI0356|5end_hypothetical_protein_326642..326872_POSITIVE 239 89 52 38 7 pint:PI2013|5end_hypothetical_protein_1972329..1972559_POSITIVE 239 90 52 78 36 pint:PI1973|5end_conserved_hypothetical_protein_1930429..1930659_POSITIVE 237 95 53 221 181 pint:PI0684|5end_coproporphyrinogen_III_oxidase_619357..619587_POSITIVE 236 93 59 73 34 pint:PI1359|5end_hypothetical_protein_1275473..1275703_POSITIVE 235 74 39 121 93 pint:PI0705|5end_conserved_hypothetical_protein;_possible_lipoprotein_641274..641504_POSITIVE 233 96 51 104 49 pint:PI1724|5end_inosine-5'-monophosphate_dehydrogenase_1641075..1641305_POSITIVE 229 80 31 191 135 pint:PI0492|5end_hypothetical_protein_451701..451931_POSITIVE 228 66 23 180 123 pint:PI1838|5end_conserved_hypothetical_protein_1780773..1781003_POSITIVE 227 80 36 72 30 pint:PI1671|5end_hypothetical_protein_1586397..1586627_POSITIVE 226 76 31 187 132 pint:PI1139|5end_endopeptidase,_endothelin-converting_enzyme_1065216..1065446_POSITIVE 226 89 58 50 13 pint:PI0930|5end_alpha-L-fucosidase_precursor_860977..861207_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 277 87 41 101 55 pint:PI0865|3end_possible_phosphoglycerol_transferase_803684..803834_POSITIVE 274 93 52 81 32 pint:PI1910|3end_hypothetical_protein_1855965..1856115_POSITIVE 263 80 33 142 89 pint:PI0040|3end_conserved_hypothetical_protein_(possible_integral_membrane_protein)_41872..42022_POSITIVE 258 100 61 51 5 pint:PI0681|3end_hypothetical_protein_619256..619406_POSITIVE 239 90 52 72 30 pint:PI1972|3end_hypothetical_protein_1930503..1930653_POSITIVE 235 74 39 131 103 pint:PI0704|3end_conserved_hypothetical_protein_641364..641514_POSITIVE 226 89 58 41 4 pint:PI0929|3end_copper_homeostasis_protein_861048..861198_POSITIVE 224 86 47 139 104 pint:PI0569|3end_phosphoglycerate_kinase_514624..514774_POSITIVE 223 90 41 100 47 pint:PI0754|3end_possible_outer_membrane_receptor_686424..686574_POSITIVE 221 100 62 111 73 pint:PI0936|3end_conserved_hypothetical_protein_869464..869614_POSITIVE 214 100 55 65 18 pint:PI2016|3end_ribosomal_large_subunit_pseudouridine_synthase_D_1974933..1975083_POSITIVE 213 100 53 101 42 pint:PI0778|3end_hypothetical_protein_714885..715035_POSITIVE 212 66 33 122 89 pint:PI0946|3end_glutathione_peroxidase_878604..878754_POSITIVE 212 93 53 151 116 pint:PI0682|3end_hypothetical_protein_619372..619522_POSITIVE 208 77 32 126 85 pint:PI0829|3end_nucleotidyl_transferase_family;_possible_mannose-1-phosphate_guanyltransferase_766539..766689_POSITIVE 208 99 58 128 82 pint:PI0606|3end_naphthoate_synthase_553917..554067_POSITIVE 208 85 49 122 87 pint:PI0356|3end_hypothetical_protein_327288..327438_POSITIVE 207 100 51 93 33 pint:PI1534|3end_ATPase/GTPase_1454166..1454316_POSITIVE 206 98 53 67 25 pint:PI1761|3end_hypothetical_protein_1684543..1684693_POSITIVE 206 87 57 125 99 pint:PI1146|3end_translation_initiation_factor_IF3_1073503..1073653_POSITIVE